Structural Studies Of Peptides Research Articles

Structure of Rhoptry Neck Protein 2 is essential for the interaction in vitro with Apical Membrane Antigen 1 in Plasmodium vivax

BackgroundIn several Apicomplexa, the formation of moving junctions (MJs) at the interface between the external membranes of the invading parasite and the host cell is essential for the process of parasite invasion. In Plasmodium falciparum and Toxoplasma gondii, the MJ is composed of the Apical Membrane Antigen 1 (AMA1) and Rhoptry Neck Proteins (RONs) complex; specifically, AMA1 interacts with RON2 during host cell invasion.MethodsRecombinant proteins based on Plasmodium vivax RON2 (A2033-P2100) and its synthetic peptide fragments, one cyclic and one linear, based on PvRON2 (D2035-T2074) were generated and used to evaluate the interaction with P. vivax AMA1 (PvAMA1) by the far western blot, surface plasmon resonance (SPR), and isothermal titration microcalorimetry (ITC) methods. The structural studies of peptides were performed by circular dichroism, and the structural analysis of the complex of PvAMA1 with peptides based on PvRON2 (D2035-T2074) was conducted with small-angle X-ray scattering (SAXS).ResultsSurface plasmon resonance (KD = 23.91 ± 2.078 μmol/L) and ITC (K = 3 × 105 mol/L) studies conclusively showed an interaction between the cyclic peptide based on PvRON2 and PvAMA1-His6. In contrast, the linear peptide and recombinant PvRON2 (GST fusion protein) did not show an interaction with PvAMA1. However, the interaction among recombinant proteins PvRON2.2 and PvAMA1-His6 was possible to show by far western blot.ConclusionsThe results show that the PvRON2 structure, particularly the S–S bond between C2051 and C2063, is determinant for the existence of the interaction between PvAMA1 and PvRON2.

Translational Diffusion Constants of Short Peptides: Measurement by NMR and Their Use in Structural Studies of Peptides

In this work, pulsed field gradient NMR is used to measure the translational self-diffusion constants (D(T)'s) of five simple peptides (GG, GR, GGR, GGNA, and GGRA) as well as glycine, G, at low concentration. The experiments were carried out in D(2)O at 298 K at pD = 3.5 in 80 mM sodium phosphate buffer. Of the five peptides, four are being reported for the first time (all except GG) and the results of G and GG are compared with D(T)'s from the literature. When corrected for differences in solvent viscosity and temperature, the discrepancy between D(T)'s of G and GG measured in the present work are lower than previously published values by several percent. Given the range of values reported in the literature for specific values of the amino acids by different groups, this discrepancy is regarded as reasonable. Diffusion constants can provide useful information about molecular size and conformation. Modeling a peptide made up of N amino acids as 2N beads (2 for each amino acid present in the peptide), we examine the diffusion constants of the above-mentioned peptides and conclude they are consistent with unfolded or random conformations in solution. Also, by comparing the diffusion constants of G and GG, an estimate of the change in solvation volume due to the loss of a water molecule can be estimated.

Bioactivity of New μ and δ Opioid Peptides

Endogenous opioids have been studied extensively since their discovery, in the hope of findings a perfect analgesic, devoid of the secondary effects of alkaloid opioids. However, the design of selective opioid agonists and or antagonists has proved very difficult. First, structural studies of peptides in general are hampered by their intrinsic flexibility. Second, the relationship between constitution and the so called "bioactive conformations" is far from obvious. Ideally, a direct structural study of the complex between a peptide and its receptor should answer both questions, but such a study is not possible, because opioids receptors are large membrane proteins, difficult to study by standard structural techniques. Thus, conformational studies of opioid peptides are still important for drug design and also for indirect receptor mapping. This review deals the pharmacological activity of : a) a new mu and deltaagonist: The single amino acid replacement of 2',6'-dimethyl-L-tyrosine in deltorphin B (H-Dmt-D-Ala-Phe-Glu-Val-Val-Gly-NH2) yielded high affinity for mu- and delta-binding sites. [Dmt1]Deltorphin B lacks activity at kappa-opioid binding sites. Bioactivity in vitro with guinea-pig ileum confirmed that [Dmt1]deltorphin B interacted with mu-opioid receptors by reducing electrically induced contractions in a naloxone-reversible manner and was 150-fold more potent than morphine and comparable to [D-Ala2,NMePhe4,Gly-ol5]enkephalin (DAGO). The inhibition of spontaneous contractions of rabbit jejunum provided evidence for delta-opioid receptor interaction. Analgesia (hot plate and tail flick tests) revealed that [Dmt1]deltorphin B was 180- to 200-fold more potent than morphine. Pretreatment with naloxone, naltrindole or H-Dmt-Tic-Ala-OH (a highly selective delta-opioid receptor antagonist) prevented [Dmt1]deltorphin B antinociception. Thus, [Dmt1]deltorphin B exhibited remarkably high dual affinity and bioactivity toward delta- and mu-opioid receptors. b) two new delta opioid peptide receptor antagonists (Dmt-Tic-OH (DTOH) and Dmt-Tic-Ala-OH (DTAOH): Dmt-Tic-OH (DTOH) and Dmt-Tic-Ala-OH (DTAOH), effective antagonists in vitro, represent a new potent opioid dipeptides for the delta-opioid receptor (Ki delta of 0.022 nM and a selectivity, Ki mu/Ki delta, of 150,000 for DTOH; Ki delta of 0.285 nM and a selectivity Ki mu/Ki delta, of 20,4 for DTAOH). In the present study we considered the pharmacological activity of these two new delta opioid peptide receptor antagonists in vivo. Therefore, we have evaluated their possible antagonistic activity against the antinociception induced by the highly selective delta opioid receptor agonist, [D-Ala2]deltorphin II (DEL). Furthermore, these two delta opioid peptide receptor antagonists were injected centrally or peripherally in order to assess their ability to act also after systemic administration. Concurrent i.c.v. injection of DTOH or DTAOH (0.5-1.0-2.0 nM) with DEL (5 nmol) induced a significant reduction of DEL antinociception. By contrast, while DTOH (10-20-40 mg/kg) administered peripherally (i.p., s.c. or i.v.) was also able to reduce DEL antinociception, DTAOH failed. The present results indicate that DTOH is the first opioid dipeptide with delta antagonist activity after systemic administration and it could be important in the clinical and therapeutic applications. c) a new mu selective opioid dipeptide antagonists: the potent delta selective opioid antagonist dipeptides were designed on the basis of a simple conformational analysis. Following a similar procedure we found a mu selective dipeptide antagonist, 2,6-dimethyl-Tyr-D-Phe-NH2. Although its selectivity is not as high as those of the quoted delta selective dipeptides it has good in vitro activity and looks very promising for further development since the 2,6-dimethyl-Tyr-D-Phe message, like the delta selective 2,6-dimethyl-Tyr-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid counterpart, seems able to impart antagonism to longer peptides.

Synthesis and structural studies of peptides containing a mannose-derived furanoid sugar amino acid

A mannose-derived furanoid sugar amino acid (Maa) induced helical turns in peptides having repeat units of Maa(Bn(2))-Phe-Leu, which aggregated into head-to-tail duplexes in the longer oligomers.

The structure of the gas-phase tyrosine–glycine dipeptide

The structural preferences of the neutral dipeptide Tyr–Gly have been investigated using a hierarchical selection scheme. This scheme consists of a hierarchy of increasingly more accurate electronic structure methods (single-point HF/3-21G* energy calculation, HF/3-21G* geometry optimization, B3LYP/6-31+G* geometry optimization, MP2/6-31+G* single-point energy calculation, and MP2/6-31+G* geometry optimization). The conformers are sorted according to their single-point or optimized energy, and only the most stable conformers according to one level are taken through to the next level of calculation. The defining structural characteristics in the 20 most stable Tyr–Gly conformers are the presence or absence of a folded arrangement of the peptide backbone (‘book’) and an OH···O hydrogen bond between the C-terminal hydroxyl group and the carbonyl oxygen of tyrosine (‘OHO’). The most stable conformer is of the book/OHO type. MP2 geometry optimization significantly alters the structure of the book-type conformers, increasing their degree of foldedness. Thus, care has to be taken when applying standard density functionals like B3LYP in structural studies of peptides with aromatic side chains.

Synthesis and structural studies of peptides containing a glucose-derived furanoid sugar amino acid

Conformational analysis of peptides containing a glucose-derived furanoid sugar amino acid (Gaa) by detailed NMR and constrained MD studies revealed that peptides with repeating Gaa-Leu-Val units had conformational signatures very similar to those of linear homooligomers of Gaa.

Natural peptide analgesics: the role of solution conformation.

Endogenous opioids have been studied extensively since their discovery, in the hope of finding a perfect analgesic, devoid of the secondary effects of alkaloid opioids. However, the design of selective opioid agonists has proved very difficult. First, structural studies of peptides in general are hampered by their intrinsic flexibility. Second, the relationship between constitution and the so-called 'bioactive conformation' is far from obvious. Ideally, a direct structural study of the complex between a peptide and its receptor should answer both questions, but such a study is not possible, because opioid receptors are large membrane proteins, difficult to study by standard structural techniques. Thus, conformational studies of opioid peptides are still important for drug design and also for indirect receptor mapping. This review deals with conformational studies of natural opioid peptides in several solvents that mimic in part the different environments in which the peptides exert their action. None of the structural investigations yields a convincing bioactive conformation, but the global conformation of longer peptides in biomimetic environments can shed light on the interaction with receptors.

Recent structural studies of peptides in Japan

Recent structural studies of peptides in Japan

Recent structural studies of peptides in Japan

Recent structural studies of peptides in Japan

Recent structural studies of peptides in Japan.

Recent x-ray structure analyses of peptides in Japan were reviewed. A series of peptides containing an aminoisobutyric acid (Aib) residue was analyzed and their helical types were investigated. Two convenient methods to determine helical types were obtained. One method was obtained by calculating averaged helical parameters and the other was obtained by investigating meridional intensity distributions. The conformations of some peptides, such as aureobasidin E, ascidiacyclamide, synthetic analogues of heat-stable enterotoxin, were studied by an x-ray diffraction method, and in some cases, with the help of nmr spectroscopy and molecular mechanics calculations. Since these peptides have physiologically important activities, the structure-activity relationships of these peptides were discussed. Several other peptide structures and the polymorphism of amino acids are also reported.

Infrared intensities of amide modes in N-methylacetamide and poly(glycine I) from a b i n i t i o calculations of dipole moment derivatives of N-methylacetamide

The infrared intensities of the amide modes in N-methylacetamide (NMA) and poly(glycine I) (PGI) have been studied using ab initio dipole moment derivatives obtained for the peptide group in NMA and an empirical force field refined for PGI. Good agreement is found between the calculated transition moment magnitudes and directions of the amide I and II modes and experimental intensity and dichroism data. By analyzing the separate contributions of each internal coordinate to the total intensity, we are able to understand in detail the origins of the IR intensities of the amide modes. Besides demonstrating one approach by which IR intensities can be studied in complex molecules and polymers, our results also provide a basis for using IR intensities in structural studies of peptides and polypeptides.